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X-RAY DIFFRACTION
Materials and Methods page
3ZC1
  •   Crystallization Hide
    Crystallization Experiments
    pH 5.5
    Details 9.5 - 10 % PEG 3K, 100 MM KCL, 200 MM MGCL2, 40 MM SODIUM CACODYLATE PH 5.5, 5 MM DTT.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 183.31 α = 90
    b = 183.31 β = 90
    c = 111.28 γ = 90
     
    Space Group
    Space Group Name:    P 42 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Details COMPOUND REFRACTIVE LENSES
    Collection Date 2010-10-01
     
    Diffraction Radiation
    Monochromator DOUBLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04
    Wavelength 0.97630
    Site DIAMOND
    Beamline I04
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.27
    Resolution(Low) 70.75
    Number Reflections(Observed) 29895
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.08
    B(Isotropic) From Wilson Plot 106.14
    Redundancy 9.2
     
    High Resolution Shell Details
    Resolution(High) 3.27
    Resolution(Low) 3.35
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.75
    Mean I Over Sigma(Observed) 2.8
    Redundancy 9.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method OTHER
    reflnsShellList 3.269
    Resolution(Low) 53.56
    Cut-off Sigma(F) 1.35
    Number of Reflections(Observed) 29852
    Number of Reflections(R-Free) 3776
    Percent Reflections(Observed) 99.88
    R-Factor(Observed) 0.2246
    R-Work 0.2205
    R-Free 0.2813
     
    Temperature Factor Modeling
    Mean Isotropic B Value 103.54
    Anisotropic B[1][1] -15.74
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -15.74
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 31.4801
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2694
    Shell Resolution(Low) 3.3108
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1932
    R-Factor(R-Work) 0.386
    R-Factor(R-Free) 0.4561
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3108
    Shell Resolution(Low) 3.3543
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1952
    R-Factor(R-Work) 0.3542
    R-Factor(R-Free) 0.3886
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3543
    Shell Resolution(Low) 3.4003
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1935
    R-Factor(R-Work) 0.3357
    R-Factor(R-Free) 0.4048
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4003
    Shell Resolution(Low) 3.4488
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1920
    R-Factor(R-Work) 0.3231
    R-Factor(R-Free) 0.4199
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4488
    Shell Resolution(Low) 3.5003
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1928
    R-Factor(R-Work) 0.309
    R-Factor(R-Free) 0.3462
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5003
    Shell Resolution(Low) 3.555
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1930
    R-Factor(R-Work) 0.2925
    R-Factor(R-Free) 0.3833
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.555
    Shell Resolution(Low) 3.6133
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1941
    R-Factor(R-Work) 0.301
    R-Factor(R-Free) 0.3811
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6133
    Shell Resolution(Low) 3.6756
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1941
    R-Factor(R-Work) 0.2923
    R-Factor(R-Free) 0.4127
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6756
    Shell Resolution(Low) 3.7424
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1931
    R-Factor(R-Work) 0.2523
    R-Factor(R-Free) 0.2816
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7424
    Shell Resolution(Low) 3.8143
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1936
    R-Factor(R-Work) 0.2373
    R-Factor(R-Free) 0.3365
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8143
    Shell Resolution(Low) 3.8922
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1931
    R-Factor(R-Work) 0.2372
    R-Factor(R-Free) 0.3258
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8922
    Shell Resolution(Low) 3.9768
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1941
    R-Factor(R-Work) 0.2345
    R-Factor(R-Free) 0.3114
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9768
    Shell Resolution(Low) 4.0693
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1916
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.2713
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0693
    Shell Resolution(Low) 4.171
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1951
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.26
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.171
    Shell Resolution(Low) 4.2837
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1944
    R-Factor(R-Work) 0.2223
    R-Factor(R-Free) 0.2778
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2837
    Shell Resolution(Low) 4.4097
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1906
    R-Factor(R-Work) 0.2168
    R-Factor(R-Free) 0.2915
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4097
    Shell Resolution(Low) 4.552
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1949
    R-Factor(R-Work) 0.2064
    R-Factor(R-Free) 0.3113
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.552
    Shell Resolution(Low) 4.7146
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1942
    R-Factor(R-Work) 0.2043
    R-Factor(R-Free) 0.2509
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7146
    Shell Resolution(Low) 4.9032
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1906
    R-Factor(R-Work) 0.2113
    R-Factor(R-Free) 0.3168
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9032
    Shell Resolution(Low) 5.1262
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1947
    R-Factor(R-Work) 0.2264
    R-Factor(R-Free) 0.2865
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1262
    Shell Resolution(Low) 5.3962
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1938
    R-Factor(R-Work) 0.2476
    R-Factor(R-Free) 0.338
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3962
    Shell Resolution(Low) 5.7339
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1916
    R-Factor(R-Work) 0.2648
    R-Factor(R-Free) 0.3227
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7339
    Shell Resolution(Low) 6.1761
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1947
    R-Factor(R-Work) 0.2273
    R-Factor(R-Free) 0.3426
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1761
    Shell Resolution(Low) 6.7965
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1930
    R-Factor(R-Work) 0.2138
    R-Factor(R-Free) 0.2419
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7965
    Shell Resolution(Low) 7.7774
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1943
    R-Factor(R-Work) 0.1676
    R-Factor(R-Free) 0.2184
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7774
    Shell Resolution(Low) 9.7889
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1915
    R-Factor(R-Work) 0.138
    R-Factor(R-Free) 0.1756
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.7889
    Shell Resolution(Low) 53.5673
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1923
    R-Factor(R-Work) 0.1944
    R-Factor(R-Free) 0.2251
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.083
    f_dihedral_angle_d 20.198
    f_angle_d 1.279
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 11807
    Nucleic Acid Atoms 0
    Heterogen Atoms 5
    Solvent Atoms 8
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XIA2, XDS
    Data Reduction (data scaling) XIA2, SCALA
    Structure Solution SNB, AUTOSHARP, PHENIX AUTOBUILD, COOT, PHENIX.REFINE, PHASER
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building PHASER
    model building PHENIX.REFINE
    model building COOT
    model building PHENIX version: AUTOBUILD
    model building AUTOSHARP
    model building SNB